Multiple sequence alignment - TraesCS7D01G106300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G106300 chr7D 100.000 3946 0 0 1 3946 64266131 64270076 0.000000e+00 7287.0
1 TraesCS7D01G106300 chr7D 90.552 3059 220 38 1 3027 64245754 64248775 0.000000e+00 3984.0
2 TraesCS7D01G106300 chr7D 86.344 3039 333 48 4 2986 63943409 63940397 0.000000e+00 3238.0
3 TraesCS7D01G106300 chr7D 92.837 2080 133 10 723 2797 59938320 59936252 0.000000e+00 3001.0
4 TraesCS7D01G106300 chr7D 97.784 1083 23 1 2864 3946 59936232 59935151 0.000000e+00 1866.0
5 TraesCS7D01G106300 chr7D 81.989 744 84 35 3238 3946 64249000 64249728 1.580000e-163 586.0
6 TraesCS7D01G106300 chr7D 86.076 158 16 5 3053 3209 64248766 64248918 8.770000e-37 165.0
7 TraesCS7D01G106300 chr7B 91.113 3038 245 15 1 3029 5503515 5506536 0.000000e+00 4091.0
8 TraesCS7D01G106300 chr7B 88.730 3008 291 27 1 2971 5282459 5285455 0.000000e+00 3633.0
9 TraesCS7D01G106300 chr7B 87.865 2810 270 41 1 2782 5216878 5219644 0.000000e+00 3234.0
10 TraesCS7D01G106300 chr7B 85.847 3116 357 57 1 3088 5337406 5340465 0.000000e+00 3234.0
11 TraesCS7D01G106300 chr7B 83.921 2270 315 34 799 3036 5320282 5322533 0.000000e+00 2124.0
12 TraesCS7D01G106300 chr7B 87.981 1664 145 37 1 1629 5510486 5512129 0.000000e+00 1914.0
13 TraesCS7D01G106300 chr7B 87.500 72 6 3 3385 3456 5506915 5506983 3.270000e-11 80.5
14 TraesCS7D01G106300 chr7A 88.990 3197 281 46 1 3164 67985451 67988609 0.000000e+00 3888.0
15 TraesCS7D01G106300 chr7A 90.771 2828 219 23 1 2797 68029502 68032318 0.000000e+00 3738.0
16 TraesCS7D01G106300 chr7A 86.652 1386 141 25 1 1354 67592666 67591293 0.000000e+00 1495.0
17 TraesCS7D01G106300 chr7A 89.883 257 21 4 3688 3940 68086412 68086667 3.800000e-85 326.0
18 TraesCS7D01G106300 chr7A 84.228 298 18 13 2862 3131 68037597 68037893 3.020000e-66 263.0
19 TraesCS7D01G106300 chr7A 79.458 443 27 16 3238 3650 68086002 68086410 5.060000e-64 255.0
20 TraesCS7D01G106300 chr7A 77.419 372 44 22 3564 3920 68038265 68038611 6.730000e-43 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G106300 chr7D 64266131 64270076 3945 False 7287.000000 7287 100.000000 1 3946 1 chr7D.!!$F1 3945
1 TraesCS7D01G106300 chr7D 63940397 63943409 3012 True 3238.000000 3238 86.344000 4 2986 1 chr7D.!!$R1 2982
2 TraesCS7D01G106300 chr7D 59935151 59938320 3169 True 2433.500000 3001 95.310500 723 3946 2 chr7D.!!$R2 3223
3 TraesCS7D01G106300 chr7D 64245754 64249728 3974 False 1578.333333 3984 86.205667 1 3946 3 chr7D.!!$F2 3945
4 TraesCS7D01G106300 chr7B 5282459 5285455 2996 False 3633.000000 3633 88.730000 1 2971 1 chr7B.!!$F2 2970
5 TraesCS7D01G106300 chr7B 5216878 5219644 2766 False 3234.000000 3234 87.865000 1 2782 1 chr7B.!!$F1 2781
6 TraesCS7D01G106300 chr7B 5337406 5340465 3059 False 3234.000000 3234 85.847000 1 3088 1 chr7B.!!$F4 3087
7 TraesCS7D01G106300 chr7B 5320282 5322533 2251 False 2124.000000 2124 83.921000 799 3036 1 chr7B.!!$F3 2237
8 TraesCS7D01G106300 chr7B 5503515 5512129 8614 False 2028.500000 4091 88.864667 1 3456 3 chr7B.!!$F5 3455
9 TraesCS7D01G106300 chr7A 67985451 67988609 3158 False 3888.000000 3888 88.990000 1 3164 1 chr7A.!!$F1 3163
10 TraesCS7D01G106300 chr7A 68029502 68032318 2816 False 3738.000000 3738 90.771000 1 2797 1 chr7A.!!$F2 2796
11 TraesCS7D01G106300 chr7A 67591293 67592666 1373 True 1495.000000 1495 86.652000 1 1354 1 chr7A.!!$R1 1353
12 TraesCS7D01G106300 chr7A 68086002 68086667 665 False 290.500000 326 84.670500 3238 3940 2 chr7A.!!$F4 702
13 TraesCS7D01G106300 chr7A 68037597 68038611 1014 False 224.000000 263 80.823500 2862 3920 2 chr7A.!!$F3 1058

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
211 212 0.028902 GTTGGACTTGACCGCACAAC 59.971 55.00 0.00 0.00 0.00 3.32 F
1788 1834 3.489047 GCTTTCAATTTTTGCGTGTGCTA 59.511 39.13 0.00 0.00 43.34 3.49 F
1905 1951 0.108615 CAGATGTTCGCGAACTCCCT 60.109 55.00 41.46 32.26 41.67 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1951 1.202867 TGCAACTTGCCTATGTCCACA 60.203 47.619 11.29 0.0 44.23 4.17 R
2590 2660 0.322546 AACTCAAGATGCCGAACCCC 60.323 55.000 0.00 0.0 0.00 4.95 R
3088 3227 1.004745 GTTGGAGGGAATGAGCCTTCA 59.995 52.381 0.00 0.0 35.86 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 1.090052 GTGCTACCATTGACCCTCGC 61.090 60.000 0.00 0.00 0.00 5.03
211 212 0.028902 GTTGGACTTGACCGCACAAC 59.971 55.000 0.00 0.00 0.00 3.32
507 508 5.259632 AGGAAATCAGTGAATTCCTTCTGG 58.740 41.667 29.44 0.00 46.23 3.86
508 509 5.014544 AGGAAATCAGTGAATTCCTTCTGGA 59.985 40.000 29.44 8.53 46.23 3.86
509 510 5.890419 GGAAATCAGTGAATTCCTTCTGGAT 59.110 40.000 26.42 9.78 42.81 3.41
648 658 4.351874 TTGTAGTGGTCCTTTTCTCTGG 57.648 45.455 0.00 0.00 0.00 3.86
693 704 4.842574 TCTTGTGCATGCACCTTATCTTA 58.157 39.130 40.01 21.41 45.63 2.10
701 725 7.435192 GTGCATGCACCTTATCTTATTTTTACC 59.565 37.037 35.69 7.64 40.79 2.85
1698 1744 5.028549 ACCATCAGTTTGATAGCACTAGG 57.971 43.478 0.00 0.00 34.28 3.02
1788 1834 3.489047 GCTTTCAATTTTTGCGTGTGCTA 59.511 39.130 0.00 0.00 43.34 3.49
1905 1951 0.108615 CAGATGTTCGCGAACTCCCT 60.109 55.000 41.46 32.26 41.67 4.20
2085 2131 2.703536 TGAAGTGCTGGAACAAGTAGGA 59.296 45.455 0.00 0.00 38.70 2.94
2338 2408 3.555917 TCTCTTCTTCTTCGTCGTTCC 57.444 47.619 0.00 0.00 0.00 3.62
2546 2616 2.289257 CGAGATGCTGCATATTCTGGGA 60.289 50.000 16.23 0.00 0.00 4.37
2597 2667 4.431131 AGCCATGCCAGGGGTTCG 62.431 66.667 0.00 0.00 30.45 3.95
2611 2681 1.087501 GGTTCGGCATCTTGAGTTCC 58.912 55.000 0.00 0.00 0.00 3.62
2787 2869 1.202114 CATCCAAAACGTCCCACCATG 59.798 52.381 0.00 0.00 0.00 3.66
2788 2870 0.474614 TCCAAAACGTCCCACCATGA 59.525 50.000 0.00 0.00 0.00 3.07
2803 2885 7.012421 GTCCCACCATGAAAATCTATTAGACAC 59.988 40.741 0.00 0.00 0.00 3.67
2876 2971 2.743664 TCTGAGCAACCATGAATTGTCG 59.256 45.455 10.29 0.00 0.00 4.35
3088 3227 1.392589 CACCGCAGCTCCCAATAAAT 58.607 50.000 0.00 0.00 0.00 1.40
3658 4014 3.300590 CCTTTTTCGCATAACATCAACGC 59.699 43.478 0.00 0.00 0.00 4.84
3870 4633 7.344352 AGCTGGAAATCTACAGAGAAATAGACT 59.656 37.037 0.00 0.00 36.86 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 6.467723 ACATCTTTTTGTAGAGCTAACACG 57.532 37.500 0.94 0.00 0.00 4.49
211 212 9.840427 AAATCAGTGTTTTAATAAGTTCATCCG 57.160 29.630 0.00 0.00 0.00 4.18
505 506 5.310331 TGATGCATACCTCTTATCCAATCCA 59.690 40.000 0.00 0.00 0.00 3.41
506 507 5.645497 GTGATGCATACCTCTTATCCAATCC 59.355 44.000 0.00 0.00 0.00 3.01
507 508 6.233434 TGTGATGCATACCTCTTATCCAATC 58.767 40.000 0.00 0.00 0.00 2.67
508 509 6.191657 TGTGATGCATACCTCTTATCCAAT 57.808 37.500 0.00 0.00 0.00 3.16
509 510 5.628797 TGTGATGCATACCTCTTATCCAA 57.371 39.130 0.00 0.00 0.00 3.53
648 658 7.205992 AGAAAGGAAGAAACAGAATTTGCTTC 58.794 34.615 0.00 0.00 31.31 3.86
693 704 5.945784 TGCAGCAGAGATAACTGGTAAAAAT 59.054 36.000 0.00 0.00 44.98 1.82
701 725 5.814764 AAGAAATGCAGCAGAGATAACTG 57.185 39.130 0.00 0.00 40.43 3.16
735 765 7.692291 CACATGAATTATTCAACCACTAACGAC 59.308 37.037 11.88 0.00 43.95 4.34
1698 1744 2.262423 AGGTCCTCACTTTTGACAGC 57.738 50.000 0.00 0.00 0.00 4.40
1788 1834 2.494870 GCTGCCACAATTTCCAAGATCT 59.505 45.455 0.00 0.00 0.00 2.75
1905 1951 1.202867 TGCAACTTGCCTATGTCCACA 60.203 47.619 11.29 0.00 44.23 4.17
1929 1975 4.262377 CCTCCTATATCCAGTGTCTGCAAG 60.262 50.000 0.00 0.00 0.00 4.01
2085 2131 5.558818 GCAATGTGAGGAGATGAGGATAAT 58.441 41.667 0.00 0.00 0.00 1.28
2338 2408 2.938956 ACCCACTTTGGAAGTCTCAG 57.061 50.000 0.00 0.00 40.96 3.35
2546 2616 4.295119 ACGGCGGCGTCAGAAACT 62.295 61.111 32.71 6.04 0.00 2.66
2590 2660 0.322546 AACTCAAGATGCCGAACCCC 60.323 55.000 0.00 0.00 0.00 4.95
2597 2667 3.135530 AGATACCTGGAACTCAAGATGCC 59.864 47.826 0.00 0.00 0.00 4.40
2601 2671 2.166459 CGCAGATACCTGGAACTCAAGA 59.834 50.000 0.00 0.00 40.72 3.02
2611 2681 2.407846 ATCGACCGCGCAGATACCTG 62.408 60.000 8.75 0.00 43.22 4.00
2787 2869 6.752351 TCAGCACTCGTGTCTAATAGATTTTC 59.248 38.462 0.00 0.00 0.00 2.29
2788 2870 6.631016 TCAGCACTCGTGTCTAATAGATTTT 58.369 36.000 0.00 0.00 0.00 1.82
2876 2971 7.148086 TGTGGTAATGAGCATATTCAGGAAAAC 60.148 37.037 0.00 0.00 35.06 2.43
3088 3227 1.004745 GTTGGAGGGAATGAGCCTTCA 59.995 52.381 0.00 0.00 35.86 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.